Nuclear magnetic resonance spectroscopy and molecular modeling studies of binding modes of cationic porphyrins to nucleic acids and peptides

Depending on the mode of binding, bound porphyrins can act as effective photosensitizers and efficiently photosensitize DNA damage. This characteristic has generated interest in the application of porphyrins in photodynamic therapy of cancer and viral infections. Two-dimensional NMR was employed to study binding in solution of aromatic cationic porphyrins to duplex and Three Way Junction (TWJ) forming DNA oligonucleotides. The NMR data shows that meso-tetrakis(4-N-methylpyridiniumyl) porphine (TMPyP4+) intercalates to the self-complementary DNA duplex d[(GCACGTGC)]2 at the central 5'-CG-3 ' site of the DNA. By molecular modeling it was shown that only a symmetrical orientation of the porphyrin at the binding site, in which two N-methylpyridiniumyl groups of the porphyrin are in each groove (2M-2m or full intercalation form), satisfies the NMR observations. The sequential assignment and molecular modeling show that binding of the porphyrin distorts the right-handed helix, but nonetheless, the normal cross-strand Watson-Crick basepairs are still formed.;By using high resolution 2D NMR (600Mhz) we showed that the cationic porphyrin meso-tetrakis(para-N-trimethylaniliniumyl)porphine (TMAP) specifically binds at the TWJ of the TWJ forming sequence 5' -GCTGCACCCGCTTGCGGCGACTTGTCGTTGTGCACG-3'. This was shown by observing differential broadening of assigned 2D NOESY crosspeaks at the junction site. This binding is a unique structure with a specific kind of intercalative binding, since this porphyrin is too large to intercalate into B-type duplex DNA. The binding is more likely stabilized by electrostatic interactions with multiple phosphate groups at the junction and by stacking with at least two of the helices.;A molecular modeling procedure was developed to calculate the inter-chromophore distance for four porphyrin/peptide complexes: TMPyP4+/YE 4, TMPyP4+/WE4, TMPyP4+/E 2YE2 and TMPyP4+/YE2(G10)E. The modeling of the pentamers complexes produced a limited set of conformational families, suggesting that the molecular modeling approach developed allows us to generate an adequate sample of the conformational space for the purpose of calculating inter-chromophore distances. The values for the inter-chromophore distances calculated from experimentally obtained parameters are in an excellent agreement with those obtained by molecular modeling, with the exception of the long peptide YE4(G10)E, for which our sampling technique is inadequate.